Information integration in molecular bioscience

Integrating information in the molecular biosciences involves more than the cross-referencing of sequences or structures. Experimental protocols, results of computational analyses, annotations and links to relevant literature form integral parts of this information, and impart meaning to sequence or structure. In this review, we examine some existing approaches to integrating information in the molecular biosciences. We consider not only technical issues concerning the integration of heterogeneous data sources and the corresponding semantic implications, but also the integration of analytical results. Within the broad range of strategies for integration of data and information, we distinguish between platforms and developments. We discuss two current platforms and six current developments, and identify what we believe to be their strengths and limitations. We identify key unsolved problems in integrating information in the molecular biosciences, and discuss possible strategies for addressing them including semantic integration using ontologies, XML as a data model, and graphical user interfaces as integrative environments.

Hierarchical indexing structure for efficient similarity search in video retrieval

With the rapid increase in both centralized video archives and distributed WWW video resources, content-based video retrieval is gaining its importance. To support such applications efficiently, content-based video indexing must be addressed. Typically, each video is represented by a sequence of frames. Due to the high dimensionality of frame representation and the large number of frames, video indexing introduces an additional degree of complexity. In this paper, we address the problem of content-based video indexing and propose an efficient solution, called the Ordered VA-File (OVA-File) based on the VA-file. OVA-File is a hierarchical structure and has two novel features: 1) partitioning the whole file into slices such that only a small number of slices are accessed and checked during k Nearest Neighbor (kNN) search and 2) efficient handling of insertions of new vectors into the OVA-File, such that the average distance between the new vectors and those approximations near that position is minimized. To facilitate a search, we present an efficient approximate kNN algorithm named Ordered VA-LOW (OVA-LOW) based on the proposed OVA-File. OVA-LOW first chooses possible OVA-Slices by ranking the distances between their corresponding centers and the query vector, and then visits all approximations in the selected OVA-Slices to work out approximate kNN. The number of possible OVA-Slices is controlled by a user-defined parameter delta. By adjusting delta, OVA-LOW provides a trade-off between the query cost and the result quality. Query by video clip consisting of multiple frames is also discussed. Extensive experimental studies using real video data sets were conducted and the results showed that our methods can yield a significant speed-up over an existing VA-file-based method and iDistance with high query result quality. Furthermore, by incorporating temporal correlation of video content, our methods achieved much more efficient performance.

ICICLE: A semantic-based retrieval system for WWW images

In this paper, we present ICICLE (Image ChainNet and Incremental Clustering Engine), a prototype system that we have developed to efficiently and effectively retrieve WWW images based on image semantics. ICICLE has two distinguishing features. First, it employs a novel image representation model called Weight ChainNet to capture the semantics of the image content. A new formula, called list space model, for computing semantic similarities is also introduced. Second, to speed up retrieval, ICICLE employs an incremental clustering mechanism, ICC (Incremental Clustering on ChainNet), to cluster images with similar semantics into the same partition. Each cluster has a summary representative and all clusters' representatives are further summarized into a balanced and full binary tree structure. We conducted an extensive performance study to evaluate ICICLE. Compared with some recently proposed methods, our results show that ICICLE provides better recall and precision. Our clustering technique ICC facilitates speedy retrieval of images without sacrificing recall and precision significantly.

Indexing and integrating multiple features for WWW images

In this paper, we present a novel indexing technique called Multi-scale Similarity Indexing (MSI) to index image's multi-features into a single one-dimensional structure. Both for text and visual feature spaces, the similarity between a point and a local partition's center in individual space is used as the indexing key, where similarity values in different features are distinguished by different scale. Then a single indexing tree can be built on these keys. Based on the property that relevant images have similar similarity values from the center of the same local partition in any feature space, certain number of irrelevant images can be fast pruned based on the triangle inequity on indexing keys. To remove the dimensionality curse existing in high dimensional structure, we propose a new technique called Local Bit Stream (LBS). LBS transforms image's text and visual feature representations into simple, uniform and effective bit stream (BS) representations based on local partition's center. Such BS representations are small in size and fast for comparison since only bit operation are involved. By comparing common bits existing in two BSs, most of irrelevant images can be immediately filtered. To effectively integrate multi-features, we also investigated the following evidence combination techniques-Certainty Factor, Dempster Shafer Theory, Compound Probability, and Linear Combination. Our extensive experiment showed that single one-dimensional index on multi-features improves multi-indices on multi-features greatly. Our LBS method outperforms sequential scan on high dimensional space by an order of magnitude. And Certainty Factor and Dempster Shafer Theory perform best in combining multiple similarities from corresponding multiple features.

Managing change and time in dynamic workflow processes

Business environments have become exceedingly dynamic and competitive in recent times. This dynamism is manifested in the form of changing process requirements and time constraints. Workflow technology is currently one of the most promising fields of research in business process automation. However, workflow systems to date do not provide the flexibility necessary to support the dynamic nature of business processes. In this paper we primarily discuss the issues and challenges related to managing change and time in workflows representing dynamic business processes. We also present an analysis of workflow modifications and provide feasibility considerations for the automation of this process.

A Correlation Analysis on LSA and HAL Semantic Space Models

In this paper, we compare a well-known semantic spacemodel, Latent Semantic Analysis (LSA) with another model, Hyperspace Analogue to Language (HAL) which is widely used in different area, especially in automatic query refinement. We conduct this comparative analysis to prove our hypothesis that with respect to ability of extracting the lexical information from a corpus of text, LSA is quite similar to HAL. We regard HAL and LSA as black boxes. Through a Pearsonrsquos correlation analysis to the outputs of these two black boxes, we conclude that LSA highly co-relates with HAL and thus there is a justification that LSA and HAL can potentially play a similar role in the area of facilitating automatic query refinement. This paper evaluates LSA in a new application area and contributes an effective way to compare different semantic space models.

Automatic texture segmentation for texture-based image retrieval

Texture-segmentation is the crucial initial step for texture-based image retrieval. Texture is the main difficulty faced to a segmentation method. Many image segmentation algorithms either can’t handle texture properly or can’t obtain texture features directly during segmentation which can be used for retrieval purpose. This paper describes an automatic texture segmentation algorithm based on a set of features derived from wavelet domain, which are effective in texture description for retrieval purpose. Simulation results show that the proposed algorithm can efficiently capture the textured regions in arbitrary images, with the features of each region extracted as well. The features of each textured region can be directly used to index image database with applications as texture-based image retrieval.

A scaleless data model for direct and progressive spatial query processing

A progressive spatial query retrieves spatial data based on previous queries (e.g., to fetch data in a more restricted area with higher resolution). A direct query, on the other side, is defined as an isolated window query. A multi-resolution spatial database system should support both progressive queries and traditional direct queries. It is conceptually challenging to support both types of query at the same time, as direct queries favour location-based data clustering, whereas progressive queries require fragmented data clustered by resolutions. Two new scaleless data structures are proposed in this paper. Experimental results using both synthetic and real world datasets demonstrate that the query processing time based on the new multiresolution approaches is comparable and often better than multi-representation data structures for both types of queries.

Extraction of texture features from arbitrary-shaped regions for image retrieval

Lots of work has been done in texture feature extraction for rectangular images, but not as much attention has been paid to the arbitrary-shaped regions available in region-based image retrieval (RBIR) systems. In This work, we present a texture feature extraction algorithm, based on projection onto convex sets (POCS) theory. POCS iteratively concentrates more and more energy into the selected coefficients from which texture features of an arbitrary-shaped region can be extracted. Experimental results demonstrate the effectiveness of the proposed algorithm for image retrieval purposes.

How does your model grow? An empirical investigation of the effects of ontological clarity and application domain size on query performance

Semantic data models provide a map of the components of an information system. The characteristics of these models affect their usefulness for various tasks (e.g., information retrieval). The quality of information retrieval has obvious important consequences, both economic and otherwise. Traditionally, data base designers have produced parsimonious logical data models. In spite of their increased size, ontologically clearer conceptual models have been shown to facilitate better performance for both problem solving and information retrieval tasks in experimental settings. The experiments producing evidence of enhanced performance for ontologically clearer models have, however, used application domains of modest size. Data models in organizational settings are likely to be substantially larger than those used in these experiments. This research used an experiment to investigate whether the benefits of improved information retrieval performance associated with ontologically clearer models are robust as the size of the application domains increase. The experiment used an application domain of approximately twice the size as tested in prior experiments. The results indicate that, relative to the users of the parsimonious implementation, end users of the ontologically clearer implementation made significantly more semantic errors, took significantly more time to compose their queries, and were significantly less confident in the accuracy of their queries.

Towards more personalized web: Extraction and integration of dynamic content from the Web

Information and content integration are believed to be a possible solution to the problem of information overload in the Internet. The article is an overview of a simple solution for integration of information and content on the Web. Previous approaches to content extraction and integration are discussed, followed by introduction of a novel technology to deal with the problems, based on XML processing. The article includes lessons learned from solving issues of changing webpage layout, incompatibility with HTML standards and multiplicity of the results returned. The method adopting relative XPath queries over DOM tree proves to be more robust than previous approaches to Web information integration. Furthermore, the prototype implementation demonstrates the simplicity that enables non-professional users to easily adopt this approach in their day-to-day information management routines.